--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/phe/variant_filters/GTFilter.py	Mon Dec 21 10:50:17 2015 -0500
@@ -0,0 +1,73 @@
+'''Filter VCF on GT filter parameter.
+
+Created on 24 Sep 2015
+
+@author: alex
+'''
+
+import argparse
+import logging
+
+from phe.variant_filters import PHEFilterBase
+
+
+class UncallableGTFilter(PHEFilterBase):
+    '''Filter uncallable genotypes'''
+
+    name = "UncallGT"
+    _default_threshold = None
+    parameter = "uncall_gt"
+
+    @classmethod
+    def customize_parser(self, parser):
+        arg_name = self.parameter.replace("_", "-")
+        parser.add_argument("--%s" % arg_name, type=str, default=self._default_threshold,
+                help="Filter sites below given GQ score (default: %s)" % self._default_threshold)
+
+    def __init__(self, args):
+        """Min Depth constructor."""
+        # This needs to happen first, because threshold is initialised here.
+        super(UncallableGTFilter, self).__init__(args)
+
+        # Change the threshold to custom gq value.
+        self.threshold = self._default_threshold
+        if isinstance(args, argparse.Namespace):
+            self.threshold = args.gq_score
+        elif isinstance(args, dict):
+            try:
+                self.threshold = str(args.get(self.parameter))
+            except (TypeError, ValueError):
+                logging.error("Could not retrieve threshold from %s", args.get(self.parameter))
+                logging.error("This parameter requires to be a string!")
+                self.threshold = None
+
+    def __call__(self, record):
+        """Filter a :py:class:`vcf.model._Record`."""
+
+        if len(record.samples) > 1:
+            logging.warn("More than 1 sample detected. Only first is considered.")
+
+        try:
+            record_gt = record.samples[0].data.GT
+        except AttributeError:
+            logging.warn("Could not retrieve GQ score POS %i", record.POS)
+            record_gt = None
+
+        if record_gt is None:
+            return "./."
+        else:
+            return None
+
+    def short_desc(self):
+        short_desc = self.__doc__ or ''
+
+        if short_desc:
+            short_desc = "%s (GT != ./. )" % (short_desc)
+
+        return short_desc
+
+    def is_gap(self):
+        return True
+
+    def is_n(self):
+        return False